How do I save warnings and errors as output from a function?

Maybe this is the same as your solution, but I wrote a factory to convert plain old functions into functions that capture their values, errors, and warnings, so I can

test <- function(i)
    switch(i, "1"=stop("oops"), "2"={ warning("hmm"); i }, i)
res <- lapply(1:3, factory(test))

with each element of the result containing the value, error, and / or warnings. This would work with user functions, system functions, or anonymous functions (factory(function(i) ...)). Here’s the factory

factory <- function(fun)
    function(...) {
        warn <- err <- NULL
        res <- withCallingHandlers(
            tryCatch(fun(...), error=function(e) {
                err <<- conditionMessage(e)
                NULL
            }), warning=function(w) {
                warn <<- append(warn, conditionMessage(w))
                invokeRestart("muffleWarning")
            })
        list(res, warn=warn, err=err)
    }

and some helpers for dealing with the result list

.has <- function(x, what)
    !sapply(lapply(x, "[[", what), is.null)
hasWarning <- function(x) .has(x, "warn")
hasError <- function(x) .has(x, "err")
isClean <- function(x) !(hasError(x) | hasWarning(x))
value <- function(x) sapply(x, "[[", 1)
cleanv <- function(x) sapply(x[isClean(x)], "[[", 1)